Biology subjects

Skoglund, P.

Publications and source records attributed to Skoglund, P..

16 recordsLinked to original sources

bioRxiv2026

Ancient DNA reveals matrilineal organisation and recurrent unions between dominant matrilines in Iron Age Britain

Kinship practices underpin all traditional societies, forming the basis for socially sanctioned reproductive unions, residence patterns and the inheritance of rights and property1,2. Although the relationship between biological relatedness and kinship is not always straightforward, ancient DNA studies are increasingly used to examine the extent to which biological relatedness underpinned social constructs of kinship in prehistoric societies3-6. Here, we report the analysis of genome-wide data for 534 individuals from the Arras Culture of Middle Iron Age northeast England (including 390 from Wetwang Slack, 100 from Pocklington, and 29 from Melton), finding evidence for communities with kinship systems structured along matrilineal lines. At Wetwang Slack, we reconstruct a 13-generation pedigree comprising 195 individuals structured around female-line connections: matrilineal transmissions greatly outnumbered patrilineal ones and male reproductive partners were largely absent from the cemetery, plausibly because they were buried in their own natal communities. Furthermore, the three main sites with robust sample sizes were characterised by non-overlapping dominant mitochondrial haplogroups, implying a maternal clan-based structure. Reproductive unions at Wetwang Slack suggest a recurrent alliance between two dominant maternal descent groups, with members of each group never reproducing with members of their own maternal lineage. Meanwhile, three individuals from lavishly furnished chariot burials at Wetwang Slack were close maternal relatives belonging to a lineage with consecutive generations of close kin unions, a pattern largely absent among other individuals at the site. These results indicate highly distinctive social practices among an elite group embedded in the wider kinship network of the Arras community.

genetics↗

bioRxiv2024

Ancient Borrelia genomes document the evolutionary history of louse-borne relapsing fever

Several disease-causing bacteria have transitioned from tick-borne to louse-borne transmission, a process associated with increased virulence and genome reduction. However, the historical time frame and speed of such evolutionary transitions have not been documented with ancient genomes. Here, we discover four ancient cases of Borrelia recurrentis, the causative agent of louse-borne relapsing fever, in Britain between [~]600 and 2,300 years ago, and sequence whole genomes up to 29-fold coverage. We estimate a recent divergence from the closest tick-borne ancestor, likely within the last [~]8,000 years. We reconstruct a chronology of gene losses and acquisitions using the pan-genome of related species, and show that almost all of the reductive evolution observed in B. recurrentis had occurred by [~]2,000 years ago, and was thus a rapid process after divergence. Our observations provide a new understanding of the origins of B. recurrentis and document complex reductive evolution in a specialist vector-borne pathogen.

evolutionary biology↗

bioRxiv2024

North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period

The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration as it connected the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7,000 BCE to 1,800 CE to study migration and mobility history in the region, with a particular focus on historically attested migrating groups during the Iron Age and the medieval period, such as Scythian, Chernyakhiv, Saltiv and Nogai associated peoples. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to present-day Western European, Eastern European, Western Steppe and East Asian groups. We also infer high heterogeneity in ancestry within geographically, culturally and socially defined groups. Despite this, we find that ancestry components which are widespread in Eastern and Central Europe have been present in the Ukraine region since the Bronze Age.

genomics↗

bioRxiv2024

High-resolution genomic ancestry reveals mobility in early medieval Europe

Ancient DNA has unlocked new genetic histories and shed light on archaeological and historical questions, but many known and unknown historical events have remained below detection thresholds because subtle ancestry changes are challenging to reconstruct. Methods based on sharing of haplotypes1,2 and rare variants3,4 can improve power, but are not explicitly temporal and have not been adopted in unbiased ancestry models. Here, we develop Twigstats, a new approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift. We apply this framework to 1,151 available ancient genomes, focussing on northern and central Europe in the historical period, and show that it allows modelling of individual-level ancestry using preceding genomes and provides previously unavailable resolution to detect broader ancestry transformations. In the first half of the first millennium [~]1-500 CE (Common Era), we observe an expansion of Scandinavian-related ancestry across western, central, and southern Europe. However, in the second half of the millennium [~]500-1000 CE, ancestry patterns suggest the regional disappearance or substantial admixture of these ancestries in multiple regions. Within Scandinavia itself, we document a major ancestry influx by [~]800 CE, when a large proportion of Viking Age individuals carried ancestry from groups related to continental Europe. This primarily affected southern Scandinavia, and was differentially represented in the western and eastern directions of the wider Viking world. We infer detailed ancestry portraits integrated with historical, archaeological, and stable isotope evidence, documenting mobility at an individual level. Overall, our results are consistent with substantial mobility in Europe in the early historical period, and suggest that time-stratified ancestry analysis can provide a new lens for genetic history.

evolutionary biology↗

bioRxiv2023

A disease-associated gene desert orchestrates macrophage inflammatory responses via ETS2

Increasing global rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1 and high failure rates during drug development2 - underscoring an urgent need to better understand disease mechanisms. Here we show how genetics could address this challenge. By investigating an intergenic haplotype on chr21q22, independently linked to inflammatory bowel disease (IBD), ankylosing spondylitis, primary sclerosing cholangitis and Takayasus arteritis3-6, we discover that the causal gene, ETS2, is a master regulator of inflammatory responses in human macrophages and delineate how the risk haplotype increases ETS2 expression. Genes regulated by ETS2 were prominently expressed in affected tissues from chr21q22-associated diseases and more enriched for IBD GWAS hits than almost all previously described pathways. Overexpressing ETS2 in resting macrophages produced an activated effector state that phenocopied intestinal macrophages from IBD7, with upregulation of multiple drug targets including TNF and IL-23. Using a database of cellular signatures8, we identify drugs that could modulate this pathway and validate the potent anti-inflammatory activity of one class of small molecules in vitro and ex vivo. Together, this highlights the potential for common genetic associations to improve both the understanding and treatment of human disease.

immunology↗

bioRxiv2023

Insufficient evidence for natural selection associated with the Black Death

Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2, for which they estimate a selection coefficient of 0.39-several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis, we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.

genomics↗

bioRxiv2022

Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers

Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe, and their consequent admixture with Mesolithic hunter-gatherers. Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus contribute to agricultural adaptations. We used genome-wide DNA from 728 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals, and to test for natural selection after admixture using a new method based on testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic ancestry in the genome (|Z| = 3.45). In contrast, we find the greatest overrepresentation of Mesolithic local ancestry across the key immunity locus that is the Major Histocompatibility Complex (MHC; |Z| > 4) which also shows allele frequency deviations indicative of a selective sweep following admixture (p =1x10-29). This could reflect negative frequency dependent selection on MHC alleles common in Neolithic populations, or that Mesolithic alleles were positively selected for and facilitated adaptation by Neolithic populations to pathogens, new diets, or other environmental factors. Our results extend previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age, and demonstrate that admixture facilitated selection by contributing new genetic variation.

evolutionary biology↗

bioRxiv2022

Yersinia pestis genomes reveal plague in Britain 4,000 years ago

Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Central Europe and Asia between 5,000 and 3,500 years before present (BP). One of these, the LNBA lineage (Late Neolithic and Bronze Age), has been suggested to have spread into Central Europe with human groups expanding from the Eurasian steppes. Here, we show that LNBA plague was spread to Europes northwestern periphery by sequencing Yersinia pestis genomes from two individuals dating to ~4,000 cal BP from an unusual mass burial context in Somerset, England, UK. This represents the earliest evidence of plague in Britain documented to date. These British Yersinia pestis genomes belong to a sublineage previously observed in two Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Central Asia ~3,600 BP. While the severity of disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility.

evolutionary biology↗

bioRxiv2021

Inferring population histories for ancient genomes using genome-wide genealogies

Ancient genomes anchor genealogies in directly observed historical genetic variation, and contextualise ancestral lineages with archaeological insights into their geography and lifestyles. We introduce an extension of the Relate algorithm to incorporate ancient genomes and reconstruct the joint genealogies of 14 previously published high-coverage ancients and 278 present-day individuals of the Simons Genome Diversity Project. As the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies, we additionally present a fast and scalable method, Colate, for inferring coalescence rates between low-coverage genomes without requiring phasing or imputation. Our method leverages sharing patterns of mutations dated using a genealogy to construct a likelihood, which is maximised using an expectation-maximisation algorithm. We apply Colate to 430 ancient human shotgun genomes of >0.5x mean coverage. Using Relate and Colate, we characterise dynamic population structure, such as repeated partial population replacements in Ireland, and gene-flow between early farmer and European hunter-gatherer groups. We further show that the previously reported increase in the TCC/TTC mutation rate, which is strongest in West Eurasians among present-day people, was already widespread across West Eurasia in the Late Glacial Period ~10k - 15k years ago, is strongest in Neolithic and Anatolian farmers, and is remarkably well predicted by the coalescence rates between other genomes and a 10,000-year-old Anatolian individual. This suggests that the driver of this signal originated in ancestors of ancient Anatolia >14k years ago, but was already absent by the Mesolithic and may indicate a genetic link between the Near East and European hunter-gatherer groups in the Late Paleolithic.

genomics↗

bioRxiv2021

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Archaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history. HighlightsO_LIWe demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remains C_LIO_LIA single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomes C_LIO_LIWe show that sediment ancient DNA can reveal important aspects of the human and faunal past C_LIO_LIEvidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum C_LIO_LI[~]0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species C_LI

developmental biology↗

bioRxiv2020

A high-coverage Neandertal genome from Chagyrskaya Cave

We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We estimate that this individual lived ~80,000 years ago and was more closely related to Neandertals in western Eurasia (1,2) than to Neandertals who lived earlier in Denisova Cave (3), which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a first view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.

genomics↗

bioRxiv2019

Insights into human genetic variation and population history from 929 diverse genomes

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

genomics↗

bioRxiv2019

Genomic approaches reveal an endemic sub-population of gray wolves in Southern China

Despite being one of the most widely distributed terrestrial mammals, the history of gray wolves (Canis lupus) in China is not well understood as their habitats have been destroyed with growing economic development. Using six specimens from wolf skins in Chinese Natural History museums, we sequenced their genome using a modified ancient DNA procedure. Using whole genome sequence analysis, we showed that gray wolves from Southern China (SC) derive from a single lineage, distinct from gray wolves from the Tibetan Plateau (Canis lupus chanco) and Northern China, suggesting that SC gray wolves may form a distinct sub-population. Of SC gray wolves, one wolf from Zhejiang carries a genetic component from a canid that must have diverged earlier from other wolves than jackals did, perhaps through gene flow from a population related to or further diverged from wolves than the dhole, a species distributed in Southern China and Southeast Asia. This may indicate that interspecific gene flow likely played an important role in shaping the speciation patterns and population structure in the genus Canis. Our study is the first to survey museum genomes of gray wolves from Southern China, revealing the presence of an endemic population with ancient interspecific gene flow from a population related to the dhole, and highlighting how sequencing the paleogenome from museum specimens can help us to study extinct species.

evolutionary biology↗

bioRxiv2018

Characterization of convergent thickening, a major convergence force producing morphogenic movement in amphibians

We characterize the morphogenic process of convergent thickening (CT), which occurs in the involuting marginal zone (IMZ) during gastrulation of Xenopus, the African clawed frog. CT was described previously as the tendency of explants of the ventral IMZ of Xenopus to converge their circumblastoporal dimension and thicken their radial dimension (Keller and Danilchik 1988). Here we show that CT occurs from the onset of gastrulation, initially throughout the pre-involution IMZ. We suggest that CT is driven by an increase in the interfacial tension between the deep IMZ and its epithelium, resulting in cells of the deep IMZ tending to minimize their surface area. In explants, this results in a progressive shortening (convergence) of the IMZ along its longer mediolateral axis and thickening in the orthogonal planes, and can generate tensile force (Shook et al. 2018). In vivo, convergence of the annular IMZ generates circumferential tension, closing the blastopore. These results provide the first clear example of a tensile morphogenic force from a Holtfreterian/Steinbergian change in tissue affinity.

developmental biology↗

bioRxiv2018

Population Turnover in Remote Oceania Shortly After Initial Settlement

Ancient DNA analysis of three individuals dated to ~3000 years before present (BP) from Vanuatu and one ~2600 BP individual from Tonga has revealed that the first inhabitants of Remote Oceania (\"First Remote Oceanians\") were almost entirely of East Asian ancestry, and thus their ancestors passed New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture with the Papuan groups they encountered [1]. However, all present-day populations in Near and Remote Oceania harbor 25-100% Papuan ancestry, implying that there must have been at least one later stream of migration eastward from Near Oceania. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu ranging from 3,000-150 BP, along with 185 present-day Vanuatu individuals from 18 islands. We show that people of almost entirely Papuan ancestry had arrived in Vanuatu by 2400 BP, an event that coincided with the end of the Lapita cultural period, changes in skeletal morphology, and the cessation of long-distance trade between Near and Remote Oceania [2]. First Remote Oceanian ancestry subsequently increased via admixture but remains at 10-20% in most islands. Through a fine-grained comparison of ancestry profiles in Vanuatu and Polynesia with diverse groups in Near Oceania, we find that Papuan ancestry in Vanuatu is consistent with deriving from the Bismarck Archipelago instead of the geographically closer Solomon Islands. Papuan ancestry in Polynesia also shows connections to the ancestry profiles present in the Bismarck Archipelago but is more similar to Tolai from New Britain and Tutuba from Vanuatu than to the ancient Vanuatu individuals and the great majority of present-day Vanuatu populations. This suggests a third eastward stream of migration from Near to Remote Oceania bringing a different type of Papuan ancestry.

genetics↗

bioRxiv2017

Paleo-Eskimo genetic legacy across North America

Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Inupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

genetics↗